WIP #25 (probably not working)

storage/storage.py

@@ -84,7 +84,9 @@ def upsert_structures(self, structures: list[dict[str, object]]) -> None:
             session.commit()
 
     # TODO this has not been tested, probably not working
-    def upsert_structures_descriptors(self, descriptors: list[dict[str, object]]) -> None:
+    def upsert_structures_descriptors(
+        self, descriptors: list[dict[str, object]]
+    ) -> None:
         with self.session(autoflush=False) as session:
             for i in range(0, len(descriptors), self.list_limit // 2):
                 session.execute(

update/generate_database_index.py

@@ -165,7 +165,7 @@ def run(path: Path) -> None:
         for rank in ranks:
             taxo_ranks.append({"id": taxon, "rank_id": rank})
     logging.info(" Processed taxa ranks")
-    
+
     storage.upsert_taxo_parenting(generate_taxon_parents_with_distance(path))
     logging.info(" Taxo parenting inserted")
     storage.upsert_triplets(triplets)